Amino acids such as aspartic acid that have two different functional groups that can associate in an amid bond formation can form two different structural arrangements in a peptide. Techniques to distinguish, for example, -aspartic from `-aspartic residues in a peptide are needed for complete structural elucidation of these peptides. We have discovered that the analysis of peptides derivatized with a fixed charge at the amino terminus by CAD-MS/MS allows us to distinguish these two isoforms of the peptide. The present study involves a comparative analysis of the CAD-MS/MS spectra of a series of isoforms peptides involving aspartic acid and glutamic acid at various sites including amino-terminus, C-terminus, and some intervening location in the peptide to determine the extent to which these alternate linkages of amid bond formation can be recognized from said spectra. The charged derivative of the peptide used in this study is the tris trimethoxytriphenylphosphonium derivative at the amino terminus of the peptide.